Redirecting stdout inside a loop Post: 302912733

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Top Forums UNIX for Dummies Questions & Answers Redirecting stdout inside a loop Post 302912733 by hmortens on Monday 11th of August 2014 03:00:15 PM

08-11-2014

Registered User

I am not familiar with VAR. But the stout.miRNA.bash.$date_formatted is where /Processed reads/ and /Trimmed reads/ comes from. It was buried in my previous posting. The first few lines of the file for the first sample are:

Code:

**testing** /illumina/runs/Runs/140513_H207_0249_AD2B9LACXX/Unaligned_Lane1/Project_DefaultProject/Sample_GRC270_DEHP2_67C/GRC270_DEHP2_67C_CGATGT_L001_R1_001.fastq.gz
/illumina/runs/Runs/140513_H207_0249_AD2B9LACXX/Unaligned_Lane1/Project_DefaultProject/Sample_GRC270_DEHP2_67C
GRC270_DEHP2_67C
cutadapt version 1.2.1
Command line parameters: -a AGATCGGAAGAGCACACGTCT -o /illumina/runs/Runs/140513_H207_0249_AD2B9LACXX/Unaligned_Lane1/Project_DefaultProject/Sample_GRC270_DEHP2_67C/GRC270_DEHP2_67C_cutadapt_AdapterRemoved.fastq.gz /illumina/runs/Runs/140513_H207_0249_AD2B9LACXX/Unaligned_Lane1/Project_DefaultProject/Sample_GRC270_DEHP2_67C/GRC270_DEHP2_67C_CGATGT_L001_R1_001.fastq.gz
Maximum error rate: 10.00%
   No. of adapters: 1
   Processed reads:      2139267
   Processed bases:    109102617 bp (109.1 Mbp)
     Trimmed reads:      2075206 (97.0%)
     Trimmed bases:     53680380 bp (53.7 Mbp) (49.20% of total)
   Too short reads:            0 (0.0% of processed reads)
    Too long reads:            0 (0.0% of processed reads)
        Total time:    155.78 s
     Time per read:      0.07 ms

=== Adapter 1 ===

Adapter 'AGATCGGAAGAGCACACGTCT', length 21, was trimmed 2075206 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20-21 bp: 2

Lengths of removed sequences
length	count	expected	max. errors
3	13563	33426.0	0
4	13593	8356.5	0
5	19992	2089.1	0
6	143974	522.3	0
7	48435	130.6	0
8	22001	32.6	0

So, you can see I only need grab a few lines using identifiers, it is just that it needs to iterate so that we get context of sample 1, sample 2, etc. and concatenated with summary.txt for each sample.
Thank you! for you help:-)

hmortens

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LEARN ABOUT DEBIAN

tqs

TQS(1)							      General Commands Manual							    TQS(1)

NAME

       tqs - Trim Quality Solexa-Illumina Sequences

SYNOPSIS

       Quality trim solexa-Illumina sequence reads using user-defined thresholds.

OPTIONS

       -h, --help
		 show this help message and exit

       -f SEQFILE, --sequence file=SEQFILE
		 Illumina sequence file - Output format from the 1G Genome Analyzer (_seq.txt):
		     7	     1	     255     669
		     AACCCCCACTCCTACAACGCCATCATTCCCCTCGAC

       -q QUALFILE, --qual file=QUALFILE
		 A prb file containing all the Illumina intensities, as outputted by the 1G Genome Analyzer (_prb.txt)

       -l MER, --length=MER
		 Length of sequence reads (i.e. Number of sequencing cycles, default=36)

       -t THRESHOLD, --threshold=THRESHOLD
		 Base intensity threshold value (-40 to 40, default=5)

       -d DIFF, --difference=DIFF
		 Base intensity difference between top intensity and second best (1 to 80, default=5)

       -c CONSEC, --consec=CONSEC
		 Minimum number of consecutive bases passing threshold values (default=20)

       -v, --verbose
		 Runs in Verbose mode.

SEE ALSO

       /usr/share/doc/ssake/TQS.readme

AUTHORS

       This  manual page was written by Andreas Tille <tille@debian.org> for the Debian system (but may be used by others).  Permission is granted
       to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by
       the Free Software Foundation.

       On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.

								   January 2008 							    TQS(1)